PMC:7252096 / 106474-108145 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T60 6-11 Body_part denotes Ileum http://purl.org/sig/ont/fma/fma7208
T61 240-245 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T62 370-374 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T63 573-577 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T64 685-689 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T65 1142-1147 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T66 1284-1288 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T67 1366-1382 Body_part denotes epithelial cells http://purl.org/sig/ont/fma/fma66768
T68 1377-1382 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T69 1484-1500 Body_part denotes epithelial cells http://purl.org/sig/ont/fma/fma66768
T70 1495-1500 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T245 6-11 Body_part denotes Ileum http://purl.obolibrary.org/obo/UBERON_0002116
T246 866-871 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T91 0-5 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T92 6-11 http://purl.obolibrary.org/obo/UBERON_0002116 denotes Ileum
T93 87-89 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T94 87-89 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T95 95-96 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T96 240-245 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T97 250-255 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T98 344-349 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T99 366-374 http://purl.obolibrary.org/obo/CLO_0008190 denotes per cell
T100 415-416 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T101 472-477 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T102 573-577 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T103 685-695 http://purl.obolibrary.org/obo/CL_0000000 denotes cell types
T104 888-889 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T105 1029-1034 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T106 1142-1147 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T107 1195-1200 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T108 1251-1255 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T109 1284-1293 http://purl.obolibrary.org/obo/CL_0000000 denotes cell type
T110 1366-1376 http://purl.obolibrary.org/obo/CL_0000066 denotes epithelial
T111 1377-1382 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T112 1413-1414 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T113 1424-1428 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T114 1484-1494 http://purl.obolibrary.org/obo/CL_0000066 denotes epithelial
T115 1495-1500 http://purl.obolibrary.org/obo/GO_0005623 denotes cells

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T62284 87-89 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T54385 760-763 Chemical denotes PCA http://purl.obolibrary.org/obo/CHEBI_36751|http://purl.obolibrary.org/obo/CHEBI_62248
T25822 1087-1090 Chemical denotes PCA http://purl.obolibrary.org/obo/CHEBI_36751|http://purl.obolibrary.org/obo/CHEBI_62248

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T764 0-11 Sentence denotes Human Ileum
T765 12-185 Sentence denotes Libraries corresponding to 13 donors were sequenced using Illumina NovaSeq S2 with a Read 1 26bp, Read 2 91bp, Index 1 8bp configuration before reads were aligned to GRCh38.
T766 186-432 Sentence denotes Each sample was filtered individually for low quality cells and genes by analyzing distributions of reads, transcripts, percent reads mapped to mitochondrial genes, and complexity per cell, then merged as an outer join to create a single dataset.
T767 433-545 Sentence denotes Clustering and differential expression tests were processed using Seurat v3.1.0 (https://satijalab.org/seurat/).
T768 546-663 Sentence denotes Normalization and variable gene selection was processed with SCTransform (https://github.com/ChristophH/sctransform).
T769 664-854 Sentence denotes Clustering for major cell types was performed using Louvain clustering on dimensionally reduced PCA space with resolution set via grid search optimizing for maximum average silhouette score.
T770 855-980 Sentence denotes Due to the scale of the dataset, a randomized subsampling from across the dataset was used to calculate the silhouette score.
T771 981-1294 Sentence denotes We annotated clusters based on highly expressed genes, then sub-clusters were characterized by performing PCA dimensionality reduction and clustering over those cells alone, and annotated based on highly expressed genes found via one-versus-rest differential expression test (Wilcoxon) within the major cell type.
T772 1295-1463 Sentence denotes Differential expression analysis between ACE2 + TMPRSS2 + and negative epithelial cells was performed in Seurat using a Wilcoxon test and Bonferroni p value correction.
T773 1464-1671 Sentence denotes Expression data for epithelial cells included in this dataset can be visualized and downloaded here: https://singlecell.broadinstitute.org/single_cell/study/SCP812?scpbr=the-alexandria-project#study-summary.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
2731 0-5 Species denotes Human Tax:9606
2735 1336-1340 Gene denotes ACE2 Gene:59272
2736 1343-1350 Gene denotes TMPRSS2 Gene:7113
2737 716-723 Chemical denotes Louvain